RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780955|ref|YP_003065368.1| hypothetical protein CLIBASIA_04270 [Candidatus Liberibacter asiaticus str. psy62] (204 letters) >2nys_A AGR_C_3712P; SSPB, stringent starvation protein B, NESG, ATR88, structural genomics, PSI-2, protein structure initiative; 2.70A {Agrobacterium tumefaciens str} SCOP: b.136.1.2 Length = 176 Score = 185 bits (471), Expect = 6e-48 Identities = 96/180 (53%), Positives = 123/180 (68%), Gaps = 13/180 (7%) Query: 25 MNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNY 84 M DHIRYDILA++ALRG+++ VL EVA+ G LPG+HHF+ITF T A GVRISQ+L+ Y Sbjct: 1 MGQDHIRYDILAQDALRGVIRKVLGEVAATGRLPGDHHFFITFLTGAPGVRISQHLKSKY 60 Query: 85 PEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHI 144 E+MTIVIQ+QFWD+KV + FE+GLSFS+ PE+LVIP+NAI+GFYDPSVNFELEFDV + Sbjct: 61 AEQMTIVIQHQFWDMKVTETGFEIGLSFSDTPEKLVIPYNAIRGFYDPSVNFELEFDVPL 120 Query: 145 EHIEEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNKNKMASVISLDNFRKK 204 EE + + + ++ K + K SV+SLD FRKK Sbjct: 121 AKEEE-------------MEEAEITAYPVSHEAKPASETPKSGEEKKEGSVVSLDAFRKK 167 >2qas_A SSPB, hypothetical protein; SSPB, adaptor, CLPX, unknown function, hydrolase activator; 2.55A {Caulobacter vibrioides} PDB: 2qaz_A Length = 157 Score = 177 bits (450), Expect = 2e-45 Identities = 57/163 (34%), Positives = 87/163 (53%), Gaps = 19/163 (11%) Query: 28 DHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEK 87 D ++Y+ +A++ALRG+VK L + A+ G LP HH YITF T A GV Q+L YP++ Sbjct: 12 DLMQYEAMAQDALRGVVKAALKKAAAPGGLPEPHHLYITFKTKAAGVSGPQDLLSKYPDE 71 Query: 88 MTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHI 147 MTIV+Q+Q+WDL + F V L F P+RL +P+ A+ FYDPSV F L+F Sbjct: 72 MTIVLQHQYWDLAPGETFFSVTLKFGGQPKRLSVPYAALTRFYDPSVQFALQFSA----- 126 Query: 148 EEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNKN 190 D+ + + +D + + ++ + Sbjct: 127 --------------PEIIEDEPEPDPEPEDKANQGASGDEGPK 155 >1ou9_A Stringent starvation protein B homolog; SSRA peptide-binding protein, homodimer, transport protein; 1.80A {Haemophilus influenzae} SCOP: b.136.1.1 PDB: 1oul_A 1zsz_C Length = 129 Score = 74.4 bits (183), Expect = 2e-14 Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 7/92 (7%) Query: 64 YITFATNARGVRISQNLRKNYPEKMTIVIQ---NQFWDLKVLDNHFEVGLSFSNVPERLV 120 Y+ GV + Y + IV+ + +L++ ++ + F V L Sbjct: 28 YLVVDATYLGVNVPVE----YVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELY 83 Query: 121 IPFNAIKGFYDPSVNFELEFDVHIEHIEEKLE 152 IP A Y + F+ + E +E Sbjct: 84 IPMGAALAIYARENGDGVMFEPEEIYDELNIE 115 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 41.1 bits (96), Expect = 2e-04 Identities = 32/190 (16%), Positives = 55/190 (28%), Gaps = 82/190 (43%) Query: 41 RGLVKVVLSE-VASI-GSLPGEHHFYITFATNAR-----G-----VRISQNLRKN----- 83 L + + + V LP I+ A+ G ++ LRK Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG 401 Query: 84 -------YPEKMTIVIQNQFWDL----------------KVLDNHFEVGLSFSNVPERLV 120 + E+ + N+F L + + + +SF+ + + Sbjct: 402 LDQSRIPFSER-KLKFSNRF--LPVASPFHSHLLVPASDLINKDLVKNNVSFN--AKDIQ 456 Query: 121 IP---------------------FNAIKGFYDPSVNFE--LEFDV-HIEHIEEKLE---G 153 IP + I P V +E +F HI L+ G Sbjct: 457 IPVYDTFDGSDLRVLSGSISERIVDCI--IRLP-VKWETTTQFKATHI------LDFGPG 507 Query: 154 GNTG-KVLTS 162 G +G VLT Sbjct: 508 GASGLGVLTH 517 Score = 29.1 bits (65), Expect = 0.75 Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 8/38 (21%) Query: 97 WDLKVLDNHFEVGLSFS------NVPERLVIPFNAIKG 128 W+ DNHF+ FS N P L I F KG Sbjct: 1646 WNRA--DNHFKDTYGFSILDIVINNPVNLTIHFGGEKG 1681 >1yfn_A Stringent starvation protein B; protein-peptide complex, SSPB, RSEA, protein binding; 1.80A {Escherichia coli} SCOP: b.136.1.1 PDB: 1ox9_A 1ox8_A Length = 118 Score = 29.3 bits (66), Expect = 0.59 Identities = 12/87 (13%), Positives = 30/87 (34%), Gaps = 3/87 (3%) Query: 64 YITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHF-EVGLSFSNVPERLVIP 122 ++ GV++ ++ ++ + I + L N F +P ++ +P Sbjct: 29 HLVVDVTLPGVQVPMEYARD--GQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVP 86 Query: 123 FNAIKGFYDPSVNFELEFDVHIEHIEE 149 A+ Y F+ + E+ Sbjct: 87 LAAVLAIYARENGAGTMFEPEAAYDED 113 >1ou8_A Stringent starvation protein B homolog; peptide-binding pocket, protein-peptide complex, homodimer, transport protein; 1.60A {Haemophilus influenzae} SCOP: b.136.1.1 PDB: 1zsz_A 1twb_A 1zsz_B Length = 111 Score = 29.2 bits (66), Expect = 0.60 Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 3/69 (4%) Query: 64 YITFATNARGVRISQNLRKNYPEKMTIVIQNQF-WDLKVLDNHFEVGLSFSNVPERLVIP 122 Y+ GV + K+ ++ + + +L++ ++ + F V L IP Sbjct: 28 YLVVDATYLGVNVPVEYVKD--GQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIP 85 Query: 123 FNAIKGFYD 131 A Y Sbjct: 86 MGAALAIYA 94 >1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2 Length = 455 Score = 26.4 bits (57), Expect = 4.4 Identities = 2/16 (12%), Positives = 9/16 (56%) Query: 17 IIKWIDTLMNYDHIRY 32 + + L++ D +++ Sbjct: 438 MTHYQALLLDTDRVQF 453 >2k8i_A SLYD, peptidyl-prolyl CIS-trans isomerase; ppiase, chaperone, rotamase; NMR {Escherichia coli} Length = 171 Score = 25.8 bits (56), Expect = 6.7 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 12/102 (11%) Query: 65 ITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFN 124 + ++ Y + ++Q D+ + + +VG+ F ++ +P Sbjct: 49 LEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAETDQGPVPVE 108 Query: 125 AIKGFYD--------PSVNFELEFDVHIEHI----EEKLEGG 154 D L+F+V + I EE+L G Sbjct: 109 ITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHG 150 >1v54_A Cytochrome C oxidase polypeptide I; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.24.1.1 PDB: 1oco_A* 1occ_A* 1ocz_A* 1ocr_A* 1v55_A* 2dyr_A* 2dys_A* 2eij_A* 2eik_A* 2eil_A* 2eim_A* 2ein_A* 2occ_A* 2zxw_A* Length = 514 Score = 25.5 bits (56), Expect = 7.7 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 14/63 (22%) Query: 16 FIIKWIDTLMNYDH----IRYDILAKEALRGLVKVVLS-----EVASIGSLPGEHHFYIT 66 FI +W+ + +H Y + A G+V LS E+ G+L G+ Y Sbjct: 2 FINRWLFST---NHKDIGTLYLLFG--AWAGMVGTALSLLIRAELGQPGTLLGDDQIYNV 56 Query: 67 FAT 69 T Sbjct: 57 VVT 59 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.319 0.135 0.402 Gapped Lambda K H 0.267 0.0578 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,805,619 Number of extensions: 81355 Number of successful extensions: 202 Number of sequences better than 10.0: 1 Number of HSP's gapped: 200 Number of HSP's successfully gapped: 19 Length of query: 204 Length of database: 5,693,230 Length adjustment: 88 Effective length of query: 116 Effective length of database: 3,559,758 Effective search space: 412931928 Effective search space used: 412931928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (24.9 bits)